New scientific evidence for the history and occupants of Tomb I (“Tomb of Persephone”) in the Great Tumulus at Vergina

The study seems to provide more info about the identity of the skeletons of the tumulus,rather than their genes.
 
Vitruvius said:
The G25 Coordinates plot most similarly to the Mycenaean Mygdalia LBA, Corsican moderns, Tsakonian Greek moderns.

View attachment 18234

The stock generic west eurasian vahaduo PCA places him between Corsicans and Central Italians but still within Mygdalia LBA Greek cluster.

View attachment 18235
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The Thracian sample from NE Bulgaria from Classical Antiquity(a female sample as 3237) seems to be the closest so far. Funny enough the 2nd one, Hungary_MidAvar:ALT-224 is a R1b-L51 sample. A coincidence, funny one considering the contamination involved.

Screenshot 2025-05-04 at 13.04.47.png
 
About the contamination
https://*****/Arkotherion/status/1919000124929278031
 

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—BoNe— said:
I have a degree in biology, and I’m a professional breeder.

Don’t copy-paste some image from the internet.

Explain in your own words how it’s even possible to contaminate the Y chromosome in ancient samples in the year 2025 — let’s see if you can articulate something coherent without embarrassing yourself.

Contamination can only ever be an issue with autosomal DNA, never with the Y chromosome.

Autosomal DNA is only useful for those PCA charts you archaeogenetics nerds like to jerk off to — people with no basic training in biology. Those of us who actually understand that 100% of autosomal DNA can be replaced in just four generations through selective breeding only care about the deep Y subclade.

In case you weren’t aware, around 95% of ancient DNA samples belong to extinct haplogroups. It’s not that they only go up to a certain subclade — they have no continuity with present-day populations. They’re extinct “cousins.”
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100% autosomal replacement in only 4 generations? Even with selection it needs more than 4 generations to erase completely an autosomal component; and selection needs some generations too to produce effects and often concerns only some targeted genes, except if you apply modern technics on the cell node. That said, 4 generations can diminish greatly a component weight (better said: somebody autosomal apport) reduced roughly to 6/7% if hazard is only in cause.
 
First of all, I apologize for being disrespectful, but I felt deeply offended by being answered by an AI in a forum that is supposed to be based on scientific rigor.

What I meant to say is this:

To say that a sample is “contaminated” implies that the issue is biologically or experimentally irreparable (for example, modern DNA significantly mixed with ancient DNA). But what often really happens is:
  • The BAM file has not been refined: certain filters have not been applied to remove contaminating, duplicated, or poorly mapped reads.
  • No damage filtering has been performed (to retain only characteristic ancient DNA reads, with deamination at the ends).
  • No authentication or cleaning process has been applied, such as PMDtools, mapDamage, or mitochondrial/Y-chromosome contamination filters.
So yes: before labeling a sample as “contaminated,” the correct approach is to check whether it simply hasn’t been properly processed or filtered.

Many public BAMs (like those from the Reich Lab or the ENA repositories) are in an “unprocessed” state and require post-processing before being used in accurate analysis. This can lead to misinterpretations if someone opens them unknowingly.

All researchers in archaeogenetics show a notable weakness in archaeology, anthropology, and cultural context. This is a general issue in these studies that must be acknowledged. None of them should be considered authorities in these areas. Archaeogeneticists are not geneticists; they are simply biologists specialized in this third semantic field, which is still under development.

For this reason, the deep Y-subclade is often left unreported in studies—not because it cannot be recovered due to low coverage. This limitation only affects the autosomes.

I have colleagues from my academic background who have worked on refining BAM files. The problem lies in the time required for filtering, not in any technical limitation in distinguishing modern contamination from authentic Y-SNPs being analyzed.
 
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MOESAN said:
100% autosomal replacement in only 4 generations? Even with selection it needs more than 4 generations to erase completely an autosomal component; and selection needs some generations too to produce effects and often concerns only some targeted genes, except if you apply modern technics on the cell node. That said, 4 generations can diminish greatly a component weight (better said: somebody autosomal apport) reduced roughly to 6/7% if hazard is only in cause.
Click to expand...

I’m going to explain how it’s possible to change 100% of an individual’s autosomal content in just 4 generations while maintaining a specific Y chromosome.

The goal is to obtain a dog that carries the characteristic Y chromosome of a German Shepherd, but whose autosomal genome is essentially that of a Boxer.
  1. First generation (F1): A male German Shepherd is crossed with a female Boxer. The resulting puppy will have 50% of its autosomes from each breed and the Y chromosome from the German Shepherd (since it’s inherited from the father).
  2. Second generation (F2): A male F1 (carrying the Shepherd Y) is crossed with another pure Boxer female who is a sister of the original Boxer from F1. The resulting puppy now has 75% or more Boxer autosomes and still carries the Shepherd Y.
  3. Third generation (F3): The process is repeated: an F2 male is crossed with another Boxer female who is a sister of the original F1 Boxer lineage. Now the puppy has ~87.5% or more Boxer autosomes, still with the Shepherd Y chromosome.
  4. Fourth generation (F4): Another cross between an F3 male and a pure Boxer female (again, a sister from the F1 Boxer generation) produces an individual with ~93.75% or more Boxer autosomes (practically indistinguishable from a pure Boxer in many traits), but still carrying the original German Shepherd Y chromosome.
This process would be impossible without introducing inbreeding—crosses must involve related individuals in order to eliminate the German Shepherd’s recessive alleles.

In these processes, there are always around 100 individuals that go unmentioned, discarded due to genetic defects. What’s actually done is selective breeding to pick the individuals with the desired autosomal traits. But in theory, this is absolutely possible and worth considering—because it’s essentially what happens in human populations: drastic genetic shifts can occur much faster than people usually think.

In selective inbreeding programs, it’s common for the genealogical tree of the final individual—after being artificially passed through a genetic bottleneck—to have only 10 real ancestors instead of the 32 that would be typical in any mammal.

If inbreeding is not used, recessive genes could accumulate up to 25% during the described process.

But by using these “knots” in the pedigree, we prevent the German Shepherd genes from reappearing generations later.
 
—BoNe— said:
I’m going to explain how it’s possible to change 100% of an individual’s autosomal content in just 4 generations while maintaining a specific Y chromosome.

The goal is to obtain a dog that carries the characteristic Y chromosome of a German Shepherd, but whose autosomal genome is essentially that of a Boxer.
  1. First generation (F1): A male German Shepherd is crossed with a female Boxer. The resulting puppy will have 50% of its autosomes from each breed and the Y chromosome from the German Shepherd (since it’s inherited from the father).
  2. Second generation (F2): A male F1 (carrying the Shepherd Y) is crossed with another pure Boxer female who is a sister of the original Boxer from F1. The resulting puppy now has 75% or more Boxer autosomes and still carries the Shepherd Y.
  3. Third generation (F3): The process is repeated: an F2 male is crossed with another Boxer female who is a sister of the original F1 Boxer lineage. Now the puppy has ~87.5% or more Boxer autosomes, still with the Shepherd Y chromosome.
  4. Fourth generation (F4): Another cross between an F3 male and a pure Boxer female (again, a sister from the F1 Boxer generation) produces an individual with ~93.75% or more Boxer autosomes (practically indistinguishable from a pure Boxer in many traits), but still carrying the original German Shepherd Y chromosome.
This process would be impossible without introducing inbreeding—crosses must involve related individuals in order to eliminate the German Shepherd’s recessive alleles.

In these processes, there are always around 100 individuals that go unmentioned, discarded due to genetic defects. What’s actually done is selective breeding to pick the individuals with the desired autosomal traits. But in theory, this is absolutely possible and worth considering—because it’s essentially what happens in human populations: drastic genetic shifts can occur much faster than people usually think.

In selective inbreeding programs, it’s common for the genealogical tree of the final individual—after being artificially passed through a genetic bottleneck—to have only 10 real ancestors instead of the 32 that would be typical in any mammal.

If inbreeding is not used, recessive genes could accumulate up to 25% during the described process.

But by using these “knots” in the pedigree, we prevent the German Shepherd genes from reappearing generations later.
Click to expand...
I'm not trying to dismiss your profession or any degrees you may or may not have, but 93.75% is quantifiably separate than the 100% replacement of which you specified. By F4 your resulting pup still does not contain 100% boxer autosomal ancestry. 93.75% may be enough to sell as a boxer breed for business purposes, but that's not really the claim nor scope of the discussion.

On a seperate note, thank you for dialing down the profanity.
 
Vitruvius said:
I'm not trying to dismiss your profession or any degrees you may or may not have, but 93.75% is quantifiably separate than the 100% replacement of which you specified. By F4 your resulting pup still does not contain 100% boxer autosomal ancestry. 93.75% may be enough to sell as a boxer breed for business purposes, but that's not really the claim nor scope of the discussion.

On a seperate note, thank you for dialing down the profanity.
Click to expand...

When we reach 90%, it’s effectively comparable to 100%. Remember that all of us here still carry between 1–3% Neanderthal or Denisovan ancestry, which is “welded in” through recessive endogamy.

Inbreeding is used to make alleles homozygous (XX) and avoid heterozygous combinations (Xx).

The process is complete when all the desired alleles are in the homozygous XX state. I’m not saying this typically happens in 4 generations—there has to be someone actively guiding the process.

To give an example: all wild horses went extinct around 10,000 BC. Humans maintained their breeding in a semi-domesticated state for 6,000 years. Today, it would take just 4 generations to achieve a 100% domesticated individual, using the process I described earlier.

That’s basically what was done by the people who spread DOM2 horses, which were later reassigned to Y-haplogroup DAC.

Mammals are not plants—Mendel’s laws are a guideline, but in mammals, you must select based on the expressed alleles of the sire and his offspring. That choice can only be made through the breeder’s judgment.

Even with the same pedigree-level inbreeding coefficients, within a single litter, one puppy may be completely free of defects while another may inherit all of them. That’s partly why many mammals have multiple offspring at once. Lions, for example, naturally maintain inbreeding levels between 12.5% and 25%.

That’s the good and bad side of inbreeding. Pharaohs bred with their sisters, but they also had a harem as a plan B—with hundreds of concubines—for when fertility between siblings failed.


What I want to convey with these writings is that you’re using PCAs to look for equivalence, when what they actually do is reveal differences.
 
@BoNe
I add let's not confuse paternal genealogy and population genetic and ethno-cultural groups. An unique Y terminal of linage, even if it's easy to trace his ancestors, cannot tell us by itself if the last bearer has/had kept on living with his brethren in their original culture or has/had switched culture, drown in another ethny. This kind of change can be more or less approached by autosomal composition even if we can often mistake.
—BoNe— said:
I’m going to explain how it’s possible to change 100% of an individual’s autosomal content in just 4 generations while maintaining a specific Y chromosome.

The goal is to obtain a dog that carries the characteristic Y chromosome of a German Shepherd, but whose autosomal genome is essentially that of a Boxer.
  1. First generation (F1): A male German Shepherd is crossed with a female Boxer. The resulting puppy will have 50% of its autosomes from each breed and the Y chromosome from the German Shepherd (since it’s inherited from the father).
  2. Second generation (F2): A male F1 (carrying the Shepherd Y) is crossed with another pure Boxer female who is a sister of the original Boxer from F1. The resulting puppy now has 75% or more Boxer autosomes and still carries the Shepherd Y.
  3. Third generation (F3): The process is repeated: an F2 male is crossed with another Boxer female who is a sister of the original F1 Boxer lineage. Now the puppy has ~87.5% or more Boxer autosomes, still with the Shepherd Y chromosome.
  4. Fourth generation (F4): Another cross between an F3 male and a pure Boxer female (again, a sister from the F1 Boxer generation) produces an individual with ~93.75% or more Boxer autosomes (practically indistinguishable from a pure Boxer in many traits), but still carrying the original German Shepherd Y chromosome.
This process would be impossible without introducing inbreeding—crosses must involve related individuals in order to eliminate the German Shepherd’s recessive alleles.

In these processes, there are always around 100 individuals that go unmentioned, discarded due to genetic defects. What’s actually done is selective breeding to pick the individuals with the desired autosomal traits. But in theory, this is absolutely possible and worth considering—because it’s essentially what happens in human populations: drastic genetic shifts can occur much faster than people usually think.

In selective inbreeding programs, it’s common for the genealogical tree of the final individual—after being artificially passed through a genetic bottleneck—to have only 10 real ancestors instead of the 32 that would be typical in any mammal.

If inbreeding is not used, recessive genes could accumulate up to 25% during the described process.

But by using these “knots” in the pedigree, we prevent the German Shepherd genes from reappearing generations later.
Click to expand...
You don't contradict me in fact. Not 100%, only if you consider some targeted and dominant visible traits in the case of your dogs. But human pop's are not dogs with strict breeding-selection process, if selection exists, is not so systhematic, so it demands more generations even if not by force a lot. Do notice I don't contradict you completely either. To date I'm not aware of an ancient pop where dominant male elite mated only with submitted female pop. But I dont' deny some washing occurred, maybe the case for Mycenians or Basques by instance.
 
Vitruvius said:
I also agree with him. Hollywood's ethnically disingenuous approach of actors portraying historical figures is nauseating. At least use actors of southern European heritage to portray ancient Greece if one isn't willing to use Greek actors themselves. The semblance will at least be there.
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To be Fair Colin Farrell looks more Southern European in his natural look.
 
HereToLearn said:
To be Fair Colin Farrell looks more Southern European in his natural look.
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Indeed, there are Northern Europeans that can look Southern. I don't think there's an issue with them playing Ancient Greeks, because it holds with authenticity. For the example the actors who played Caesar and Mark Antony in HBO's Rome were good and convincing. What I do find troubling is that some people will claim that they are literally Irish/Anglo-like (genetically) as an effort to facilitate an ethno-nationalistic flex against the actual descendants of Ancient Greeks.

Also, it is worth mentioning, that there were Ancient Greeks that did look Northern (Light eyes and hair) but genetically they were typical Greeks. It is astounding that in 2025. Even after over 10 year of aDNA, there's still some people who cannot comprehend that there's some phenotyic overlaps between Northern and Southern Europeans. Or even Southern Europeans and Near easterners. Yet can still be distinguishable genetically, as well as the fact that all three of them have some overlap via ancient populations.


X is really abysmal with this type of ignorance due to the massive audience of ideologically driven users, but I hold eupedia to a higher standard for genetic knowledge.
 
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Jovialis said:
Indeed, there are Northern Europeans that can look Southern. I don't think there's an issue with them playing Ancient Greeks, because it holds with authenticity. For the example the actors who played Caesar and Mark Antony in HBO's Rome were good and convincing. What I do find troubling is that some people will claim that they are literally Irish/Anglo-like as an effort to facilitate an ethno-nationalistic flex against the actual descendants of Ancient Greeks.
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Colin Farrel can pass overall in Balkans and Mediterranean, i would argue his natural hair color would have been better at the role rather than dying so blonde. Another case is Sean Connery.

The Welsh actor Ioan Gruffudd who played in King Arthur 2004 could play any Southern European looking role. I can picture him playing a Roman general of some sort since he looks a bit more Western Med.

17e3718589ef-ioan-gruffudd.jpg
 
HereToLearn said:
To be Fair Colin Farrell looks more Southern European in his natural look.
Click to expand...

Colin Farrell's look in Ireland (and even in Great Britain) is less anomalous than one might think. it's just that there is this cliché that all Northern Europeans have to be 2 metres tall, very robust with blue eyes and blond hair, to be considered as such.
 
Pax Augusta said:
Colin Farrell's look in Ireland (and even in Great Britain) is less anomalous than one might think. it's just that there is this cliché that all Northern Europeans have to be 2 metres tall, very robust with blue eyes and blond hair, to be considered as such.
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You are absolutely right. My point is that I find less disturbing to see a reasonably Southern European-looking Northern European like Colin Farrell play a Southern European character than the fact that in Hollywood (modern) Southern Europeans' spectrum goes from Dustin Hoffman to Al Pacino or from Penelope Cruz to Monica Bellucci, as Jovialis points out (internationally known Greek actors don't occur to me, sorry).
 
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HereToLearn said:
You are absolutely right. My point is that I find less disturbing to see a reasonably Southern European-looking Northern European like Colin Farrell play a Southern European character than the fact that in Hollywood (modern) Southern Europeans' spectrum goes from Dustin Hoffman to Al Pacino, as Jovialis points out.
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Hollywood has always been the greatest producer of stereotypes and clichés, reflecting those prevalent and rooted in American society. So I never expect anything good.
 
I see that the thread has veered off a bit. It's is unfortunate that the samples were contaminated and we cannot derive any genetic information from them. Even if we had unspoiled DNA it would tell us only what the elite's genetic makeup was like. Where were the common folk buried? Were they all cremated? I know that it's easier for archaeologists to dig around the great palaces, not to mention the prestige it brings. From the genetic point of view there are probably a lot more bones of common folk than of their leaders.
 
bigsnake49 said:
I see that the thread has veered off a bit. It's is unfortunate that the samples were contaminated and we cannot derive any genetic information from them. Even if we had unspoiled DNA it would tell us only what the elite's genetic makeup was like. Where were the common folk buried? Were they all cremated? I know that it's easier for archaeologists to dig around the great palaces, not to mention the prestige it brings. From the genetic point of view there are probably a lot more bones of common folk than of their leaders.
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Only the DEM3237 is not contaminated according to the supplementary
 
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